[Chimera-users] want to converge 20 pdb files of a trimer

ashok rout ashok9869 at gmail.com
Mon Oct 7 17:16:23 PDT 2013


Hi Elaine,
 Thanks a lot. Now it is working.
Regards,
Ashok


On Mon, Oct 7, 2013 at 4:08 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Ashok,
> As I said, you have to use the match command 19 times because it will only
> make a pairwise match.  You have to decide which one you want to use as the
> reference and then match each of the other 19 to the reference in a
> separate match command.
>
> Also, your first command is wrong, should contain "-" instead of "," to
> use all the residues from 379 to 400 (instead of only two residues, 379 and
> 400). For example, if you want to make #0 the reference:
>
> match #1:379-400 #0:379-400
> match #2:379-400 #0:379-400
> [ ... etc. 18 more times ...]
>
> The above is if you had each NMR structure in its own separate PDB file.
> Usually NMR structures in the PDB are all in one file.  In that case, it
> would be something like:
>
> match #0.2:379-400 #0.1:379-400
> match #0.3:379-400 #0.1:379-400
> [ ... etc. 18 more times ...]
>
> Elaine
>
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic
> >
>
> On Oct 7, 2013, at 3:57 PM, ashok rout wrote:
>
> > Hi Elaine,
> > Thanks for your reply. I am able to superimpose 2 pbd files by using
> command "match #0:379,400 #1:379,400", where #0 and #1 are 1st and 2nd pdb
> files. 379, 400 means I want to superimpose residues from 379 to 400.
> >  After that I have problem (error: an even number of space-separated
> atom specs are required) when I am trying to superimpose 3 pdb files using
> command "match #0:379,400 #1:379,400 #2:379,400".
> >
> > I am clearly writing you:
> > I have 20 pdb files of the trimer. e.g 1.pdb, 2.pdb, 3.pdb .... 20.pdb
> > Residues in the pdb file is from 369-410. I want to superimpose residues
> from 379-400.
> > So what exactly the commands and steps.
> > Thanks,
> > Ashok
> >
> >
> > On Mon, Oct 7, 2013 at 3:21 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Ashok,
> > Not sure exactly what you mean by "converge" ...
> >
> > (A) If you mean to superimpose (to put on top of each other), you would
> probably want to use either MatchMaker or the command "match."  The
> different methods for superimposing structures are described in this page
> and its links:
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> >
> > With the "match" command you specify exactly which residues/atoms to use
> in the match. You would have to use it 19 times with the same single
> structure as reference (e.g. to superimpose 0.1 and 0.2, then 0.1 and 0.3,
> ...)
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic
> >
> >
> > Matchmaker only uses CA atoms and doesn't require specifying which
> residues to use, but optionally you can restrict it to use only a certain
> section with the "Further restrict matching to current selection" option.
>  You can choose one structure as reference and the other 19 as structures
> to match.
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html
> >
> >
> > (B) If you mean to calculate an average, you can do that with the MD
> Movie tool, after opening the NMR file as a trajectory:
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html
> >
> >
> > 1. download the NMR structure PDB file to some location on your computer
> that you will be able to find later
> > 2. start MD Movie (in menu under Tools... MD/Ensemble Analysis)
> > 3. choose to open "PDB, single file" and browse to open the NMR
> structure file
> > 4. from the MD Movie menu, choose "Analysis... Average Structure"
> >
> > Be aware this is a simple Cartesian coordinate average and the result
> may be distorted. I don't think you can average just some part. Just
> average the whole thing and then you can delete the parts you don't want
> later.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > On Oct 7, 2013, at 2:38 PM, ashok rout wrote:
> >
> > > Hi,
> > >  I have a nmr structure of a protein which is a trimer. I want to
> converge 20 pdb files of the trimer, by Chimera. And also want to converge
> a specific region of the 20 pdb files of the trimer.
> > > Can you please assist me how to do this??
> > > Thanks,
> > > Ashok
> >
> >
> >
> >
> > --
> > thanks & regards,
> > Ashok
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>


-- 
thanks & regards,
Ashok
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